Flexible circuits typically consist of a polymer substrate and patterned conductive layer on the polymer substrate. Some flexible circuits additionally have protective cover layers. The cover layers are typically pre-patterned polymer films that are placed over the patterned conductive layer and adhered to the polymer substrate layer. The cover layers are patterned so that only portions of the conductive layer are exposed. Adequate application of these cover layers requires precise registration of the cover layer to the flexible circuit as it is applied. If misregistration occurs, an incorrect portion of the conductive layer will be exposed, potentially rendering the flexible circuit defective or useless.